stoppedFlow
Class StoppedFlow

java.lang.Object
  java.awt.Component
      java.awt.Container
          java.awt.Panel
              java.applet.Applet
                  edu.davidson.tools.SApplet
                      stoppedFlow.StoppedFlow

All Implemented Interfaces:

edu.davidson.tools.SDataSource, edu.davidson.tools.SStepable, java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, javax.accessibility.Accessible

public class StoppedFlow
extends edu.davidson.tools.SApplet
implements edu.davidson.tools.SStepable, edu.davidson.tools.SDataSource

This applet simulates a stopped-flow apparatus for performing kinetics studies. This applet functions as a data source in SDataSource, providing real-time data for time, absorbance (A), dA/dt, and concentrations (C) and dC/dt for the various species in the system. The rate law can be user-defined.

This applet uses Data Connections.

Applet Parameters

NAME	Variable Type	Default	Description
BGColor	String	null	The string is converted to an integer representing the RGB color to be used as the background color for the applet.
CalculationOnly	boolean	false	If true, no image is displayed in the applet area and no animation is performed. The applet performs only the calculation.
CellLength	double	0.5	The cell path length is used in computing the absorbance reading
Dt	double	0.050	This is the time interval in seconds for the animation. The smaller this value the smoother the animation provided the CPU is sufficiently fast.
IsReady	String		JavaScript variable that will be set to true when applet has initialized. Must use MAYSCRIPT in APPLET tag to use this feature.
IsVertical	boolean	false	If true the stopped flow apparatus is oriented vertically; otherwise the orientation is horizontal.
SyringeHeight	int	0	Sets the height of the syringe body in pixels. If a value of zero (the default) is supplied, the height of the syringe is scaled to fit the available space.
SyringeWidth	int	0	Sets the width of the syringe body in pixels. If a value of zero (the default) is supplied, the width of the syringe is scaled to fit the available space.
TubeWidth	int	10	Sets the width in pixels of the tubes in the stopped flow apparatus.

Version:

2.0

Author:

David N. Blauch

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class java.awt.Component

java.awt.Component.BaselineResizeBehavior

Field Summary

Fields inherited from class edu.davidson.tools.SApplet

clock, dataConnections, dataListeners, dataSources, lock

Fields inherited from class java.awt.Component

BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT

Fields inherited from interface java.awt.image.ImageObserver

ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

Constructor Summary

StoppedFlow()

Method Summary

void	clearCoefficients() Sets all stoichiometric coefficients to zero, except for that of species 0, which is set to -1.
void	clearColors() Sets the color for all species to the background color
void	clearConcentrationsA() Sets the concentrations of all species in the syringe A solution to zero.
void	clearConcentrationsB() Sets the concentrations of all species in the syringe B solution to zero.
void	clearMolarAbsorptivities() Sets all molar absorptivities to zero.
void	clearRateLaw() Sets all exponents in the rate law to zero.
void	destroy()
double	getAbsorbance(double[] _conc) Returns the absorbance for a set of molar concentrations.
double[]	getAbsorbanceDataSet() Returns the absorbance data set from the last simulation.
double	getAbsorbanceDataSet(int _i) Returns the absorbance at index _i.
java.lang.String	getAppletInfo()
java.awt.Color	getColor(double[] _conc) Returns the color for a set of concentrations.
java.awt.Color	getColor(int _red, int _green, int _blue) Returns the color with the indicated red, green, and blue components.
double[][]	getDataSet() Returns the data set from the last simulation.
double[]	getDataSet(int _n) Returns the data set for species _n.
double	getDataSet(int _n, int _i) Returns the concentration of species _n at index _i.
edu.davidson.tools.SApplet	getOwner() Gets the owner of the data source.
java.lang.String	getParameter(java.lang.String key, java.lang.String def)
java.lang.String[][]	getParameterInfo()
double[][]	getVariables() Gets the values of the variables for SDataSource. element [0][0] is the time as provided by the timer, which might be disabled element [0][1] is the number of photons emitted by the light source element [0][2] is the number of photons detected by the detector element [0][3] is the intensity (photons/sec), which is zero if the timer is off element [0][4] is the transmittance, which is zero if the timer is off element [0][5] is the absorbance, which is zero if the timer is off The transmittance and absorbance are determined using the reference intensity, if it is defined; otherwise the source intensity is used.
java.lang.String[]	getVarStrings() Returns an array of the variable names supplied by this SDataSource. t is the simulation time in seconds A is the absorbance C0 through C7 are concentrations of species 0 through 7
void	init()
boolean	isRunning() Returns true is a simulation is running.
void	paint(java.awt.Graphics g)
void	resetSimulation() Resets the simulation.
void	setCalculationOnly(boolean _calcOnly) Sets the calculation only flag.
void	setCellPathLength(double _length) Sets the cell path length (in centimeters)
void	setCoefficient(int _n, double _coef) Sets the stoichiometric coefficient for a single species.
void	setCoefficients(double[] _coef) Sets the stoichiometric coefficients for each species.
void	setColor(int _n, java.awt.Color _color) Sets the color of a single species.
void	setColor(int _n, java.lang.String _color) Sets the color of a single species.
void	setColors(java.awt.Color _color) Sets the color of all species to the indicated color.
void	setColors(java.awt.Color[] _colors) Sets the colors of all species.
void	setColors(java.lang.String _color) Sets the color of all species to the indicated color.
void	setColors(java.lang.String[] _colors) Sets the colors of all species.
void	setConcentrationA(int _n, double _conc) Sets the molar concentration of a single species in the liquid in syringe A.
void	setConcentrationB(int _n, double _conc) Sets the molar concentration of a single species in the liquid in syringe B.
void	setConcentrations(double[] _concA, double[] _concB) Sets the molar concentrations of species in the liquid in syringes.
void	setConcentrationsA(double[] _conc) Sets the molar concentrations of species in the liquid in syringe A.
void	setConcentrationsB(double[] _conc) Sets the molar concentrations of species in the liquid in syringe B.
void	setFractions(double _fractionA, double _fractionB) Sets the initial fractions of the total syringe volumes.
void	setFractionsDelivered(double _fractionA, double _fractionB) Sets the fractions of the total syringe volumes that are delivered in the simulation.
void	setLightColor(java.awt.Color _color) Sets the light color.
void	setLightColor(double _wavelength) Sets the light beam to the color corresponding with the indicated wavelength.
void	setMinimumStepSize(double _hmin) Sets the minimum step size in seconds for the Fourth Order Runge-Kutta-Fehlberg algorithm.
void	setMolarAbsorptivities(double[] _molAbs) Sets the molar absorptivities of the various species.
void	setMolarAbsorptivity(int _n, double _molAbs) Sets the molar absorptivity of a single species.
void	setOutputIncrement(double _dt) Sets the output increment for simulation data.
void	setOwner(edu.davidson.tools.SApplet owner) Sets the owner for the SDataSource.
void	setPrecision(double _tol) Sets the relative precision for the numerical calculations for the user-defined reaction order.
void	setRandom(long rnd) Sets the seed value for the random number generator.
void	setRateConstant(double _rateConstant) Sets the rate constant based upon species 0.
void	setRateLaw(double[] _exp) Sets the rate law for the user-defined kinetics option (see setReactionOrder).
void	setRateLaw(int _n, double _exp) Sets the exponent in the rate law for a given species for the user-defined kinetics option (see setReactionOrder).
void	setReactionOrder(int _rxnOrder) Sets the reaction order for the kinetics.
void	setStandardDeviation(double _std) Sets the standard deviation for the Gaussian error applied to the absorbance.
void	setStartTime(double _time) Sets the starting time for the chemical reaction.
void	setStopTime(double _time) Sets the stopping time for the simulation reaction.
void	setTimeIncrement(double _dt) Sets the time increment for the simulation.
void	start()
void	startSimulation() Starts the simulation.
void	step(double dt, double tm) Calculates state of system at each step in the simulation.
void	stop()
void	stopSimulation() Stops the simulation.

Methods inherited from class edu.davidson.tools.SApplet

addDataListener, addDataSource, cleanupDataConnections, clearAllData, clearData, deleteDataConnection, deleteDataConnections, forward, getClockID, getClockTime, getDataConnectionFromDL, getDataConnectionFromDS, getDataFromDS, getDataListener, getDataListener, getDataSource, getDataSource, getID, getRunningID, getSourceData, getSourceVariables, isAutoRefresh, isClockRunning, makeDataConnection, pause, removeDataListener, removeDataSource, reset, reverse, setAutoRefresh, setClockContinous, setClockCycle, setClockOneShot, setClockTime, setConnectionBlock, setConnectionListener, setConnectionSmoothing, setConnectionSource, setConnectionStride, setDefault, setDt, setExternalClock, setFPS, setRunningID, setRunningID, setTimeContinuous, setTimeCycle, setTimeOneShot, startClock, stepClock, stepTime, stepTimeBack, stepTimeForward, stopClock, updateDataConnection, updateDataConnections

Methods inherited from class java.applet.Applet

getAccessibleContext, getAppletContext, getAudioClip, getAudioClip, getCodeBase, getDocumentBase, getImage, getImage, getLocale, getParameter, isActive, newAudioClip, play, play, resize, resize, setStub, showStatus

Methods inherited from class java.awt.Panel

addNotify

Methods inherited from class java.awt.Container

add, add, add, add, add, addContainerListener, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getAlignmentX, getAlignmentY, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getInsets, getLayout, getListeners, getMaximumSize, getMinimumSize, getMousePosition, getPreferredSize, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, print, printComponents, remove, remove, removeAll, removeContainerListener, removeNotify, setComponentZOrder, setFocusCycleRoot, setFocusTraversalKeys, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setFont, setLayout, transferFocusBackward, transferFocusDownCycle, update, validate

Methods inherited from class java.awt.Component

action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, contains, contains, createImage, createImage, createVolatileImage, createVolatileImage, disable, dispatchEvent, enable, enable, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBaseline, getBaselineResizeBehavior, getBounds, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getGraphics, getGraphicsConfiguration, getHeight, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocation, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getSize, getToolkit, getTreeLock, getWidth, getX, getY, gotFocus, handleEvent, hasFocus, hide, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isDoubleBuffered, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isOpaque, isPreferredSizeSet, isShowing, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, postEvent, prepareImage, prepareImage, printAll, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, repaint, requestFocus, requestFocusInWindow, reshape, setBackground, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setLocation, setLocation, setMaximumSize, setMinimumSize, setName, setPreferredSize, setSize, setSize, setVisible, show, show, size, toString, transferFocus, transferFocusUpCycle

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface edu.davidson.tools.SDataSource

getID

Constructor Detail

StoppedFlow

public StoppedFlow()

Method Detail

getParameter

public java.lang.String getParameter(java.lang.String key,
                                     java.lang.String def)

init

public void init()

Overrides:

init in class java.applet.Applet

start

public void start()

Overrides:

start in class java.applet.Applet

startSimulation

public void startSimulation()

Starts the simulation. If a simulation has previously been run or parameters have been changed, it is necessary to reset the simulation prior to starting a new simulation.

See Also:

stopSimulation()

stop

public void stop()

Overrides:

stop in class java.applet.Applet

stopSimulation

public void stopSimulation()

Stops the simulation.

See Also:

startSimulation()

destroy

public void destroy()

Overrides:

destroy in class edu.davidson.tools.SApplet

getAppletInfo

public java.lang.String getAppletInfo()

Overrides:

getAppletInfo in class java.applet.Applet

getParameterInfo

public java.lang.String[][] getParameterInfo()

Overrides:

getParameterInfo in class java.applet.Applet

clearCoefficients

public void clearCoefficients()

Sets all stoichiometric coefficients to zero, except for that of species 0, which is set to -1.

clearColors

public void clearColors()

Sets the color for all species to the background color

clearConcentrationsA

public void clearConcentrationsA()

Sets the concentrations of all species in the syringe A solution to zero.

clearConcentrationsB

public void clearConcentrationsB()

Sets the concentrations of all species in the syringe B solution to zero.

clearMolarAbsorptivities

public void clearMolarAbsorptivities()

Sets all molar absorptivities to zero.

clearRateLaw

public void clearRateLaw()

Sets all exponents in the rate law to zero.

getAbsorbance

public double getAbsorbance(double[] _conc)

Returns the absorbance for a set of molar concentrations. Random error is NOT added to this value.

getAbsorbanceDataSet

public double[] getAbsorbanceDataSet()

Returns the absorbance data set from the last simulation. The user is expected to reconstruct the times, which are the index*(output time interval). This absorbance data, like the data supplied to DataConnections, has random error added.

getAbsorbanceDataSet

public double getAbsorbanceDataSet(int _i)

Returns the absorbance at index _i. The time is _i*(output time interval) This absorbance data, like the data supplied to DataConnections, has random error added.

getColor

public java.awt.Color getColor(int _red,
                               int _green,
                               int _blue)

Returns the color with the indicated red, green, and blue components. Each component has a value between 0 and 255.

getColor

public java.awt.Color getColor(double[] _conc)

Returns the color for a set of concentrations. Should be called after the simulation is reset, so changes in colors take effect.

getDataSet

public double[][] getDataSet()

Returns the data set from the last simulation. The user is expected to reconstruct the times, which are the index*(output time interval)

getDataSet

public double[] getDataSet(int _n)

Returns the data set for species _n. The user is expected to reconstruct the times, which are the index*(output time interval)

getDataSet

public double getDataSet(int _n,
                         int _i)

Returns the concentration of species _n at index _i. The time is _i*(output time interval)

getOwner

public edu.davidson.tools.SApplet getOwner()

Gets the owner of the data source.

Specified by:

getOwner in interface edu.davidson.tools.SDataSource

Returns:

owner of the data source, which is this applet

getVariables

public double[][] getVariables()

Gets the values of the variables for SDataSource.
element [0][0] is the time as provided by the timer, which might be disabled
element [0][1] is the number of photons emitted by the light source
element [0][2] is the number of photons detected by the detector
element [0][3] is the intensity (photons/sec), which is zero if the timer is off
element [0][4] is the transmittance, which is zero if the timer is off
element [0][5] is the absorbance, which is zero if the timer is off
The transmittance and absorbance are determined using the reference intensity, if it is defined; otherwise the source intensity is used.

Specified by:

getVariables in interface edu.davidson.tools.SDataSource

Returns:

a one-by-three array

getVarStrings

public java.lang.String[] getVarStrings()

Returns an array of the variable names supplied by this SDataSource.
t is the simulation time in seconds
A is the absorbance
C0 through C7 are concentrations of species 0 through 7

Specified by:

getVarStrings in interface edu.davidson.tools.SDataSource

paint

public void paint(java.awt.Graphics g)

Overrides:

paint in class java.awt.Container

isRunning

public boolean isRunning()

Returns true is a simulation is running.

resetSimulation

public void resetSimulation()

Resets the simulation. This method should be run before beginning a new simulation.

setCalculationOnly

public void setCalculationOnly(boolean _calcOnly)

Sets the calculation only flag. If true, no image is displayed and no animation is performed. The applet only calculates the data in the time interval t = 0 to the stop time (in seconds). The calculation does not occur in real time. The normal operation of the applet corresponds with this value being false.

setCellPathLength

public void setCellPathLength(double _length)

Sets the cell path length (in centimeters)

setCoefficient

public void setCoefficient(int _n,
                           double _coef)

Sets the stoichiometric coefficient for a single species. The stoichiometric coefficient for species 0 cannot be zero; it must be negative. Reactants have negative stoichiometric coefficients; products have positive stoichiometric coefficients. This method should not be called while a simulation is running.

Parameters:

_n - species number (0 through 7)

_coef - stoichiometric coefficient

setCoefficients

public void setCoefficients(double[] _coef)

Sets the stoichiometric coefficients for each species. The stoichiometric coefficient for species 0 cannot be zero; it must be negative. Reactants have negative stoichiometric coefficients; products have positive stoichiometric coefficients. This method should not be called while a simulation is running.

setColor

public void setColor(int _n,
                     java.awt.Color _color)

Sets the color of a single species.

Parameters:

_n - species number (0 through 7)

_color - color of species

setColor

public void setColor(int _n,
                     java.lang.String _color)

Sets the color of a single species.

Parameters:

_n - species number (0 through 7)

_color - string containing a RGB number, e.g., #FF00FF

setColors

public void setColors(java.awt.Color _color)

Sets the color of all species to the indicated color.

setColors

public void setColors(java.lang.String _color)

Sets the color of all species to the indicated color.

Parameters:

_color - string containing a RGB number, e.g., #FF00FF

setColors

public void setColors(java.awt.Color[] _colors)

Sets the colors of all species.

setColors

public void setColors(java.lang.String[] _colors)

Sets the colors of all species.

Parameters:

_color - array of strings containing a RGB numbers, e.g., #FF00FF

setConcentrationA

public void setConcentrationA(int _n,
                              double _conc)

Sets the molar concentration of a single species in the liquid in syringe A.

Parameters:

_n - species number (0 through 7)

_conc - molar concentration

See Also:

setConcentrationB(int, double)

setConcentrationsA

public void setConcentrationsA(double[] _conc)

Sets the molar concentrations of species in the liquid in syringe A. The simulation provides for eight concentrations. Additions array elements are disregarded; missing array elements are given a value of zero.

See Also:

setConcentrationsB(double[]), setConcentrations(double[], double[])

setConcentrationB

public void setConcentrationB(int _n,
                              double _conc)

Sets the molar concentration of a single species in the liquid in syringe B.

Parameters:

_n - species number (0 through 7)

_conc - molar concentration

See Also:

setConcentrationA(int, double)

setConcentrationsB

public void setConcentrationsB(double[] _conc)

Sets the molar concentrations of species in the liquid in syringe B. The simulation provides for eight concentrations. Additions array elements are disregarded; missing array elements are given a value of zero.

See Also:

setConcentrationsA(double[]), setConcentrations(double[], double[])

setConcentrations

public void setConcentrations(double[] _concA,
                              double[] _concB)

Sets the molar concentrations of species in the liquid in syringes. The simulation provides for eight concentrations. Additions array elements are disregarded; missing array elements are given a value of zero.

Parameters:

_concA - array containing concentrations of species in syringe A

_concB - array containing concentrations of species in syringe B

See Also:

setConcentrationsA(double[]), setConcentrationsB(double[])

setFractions

public void setFractions(double _fractionA,
                         double _fractionB)

Sets the initial fractions of the total syringe volumes.

Parameters:

_fractionA - fraction of total volume of syringe A

_fractionB - fraction of total volume of syringe B

See Also:

setFractionsDelivered(double, double)

setFractionsDelivered

public void setFractionsDelivered(double _fractionA,
                                  double _fractionB)

Sets the fractions of the total syringe volumes that are delivered in the simulation. The fractions must lie between 0.1 and 1.0. The user must arbitrarily decide the total volume of liquid contained in each syringe. The simulation must not be running when this method is called. The initial volumes of each syringe should be set prior to calling this method.

Parameters:

_fractionA - fraction of total volume of syringe A delivered

_fractionB - fraction of total volume of syringe B delivered

See Also:

setFractions(double, double)

setMolarAbsorptivity

public void setMolarAbsorptivity(int _n,
                                 double _molAbs)

Sets the molar absorptivity of a single species. Units should be in L / (mole cm)

Parameters:

_n - species number (0 through 7)

_molAbs - molar absorptivity

setLightColor

public void setLightColor(double _wavelength)

Sets the light beam to the color corresponding with the indicated wavelength.

Parameters:

_wavelength - wavelength in nanometers (must lie between 380 and 780 nm)

setLightColor

public void setLightColor(java.awt.Color _color)

Sets the light color.

setMinimumStepSize

public void setMinimumStepSize(double _hmin)

Sets the minimum step size in seconds for the Fourth Order Runge-Kutta-Fehlberg algorithm. Default is 0.00001 sec.

setMolarAbsorptivities

public void setMolarAbsorptivities(double[] _molAbs)

Sets the molar absorptivities of the various species. Units should be in L / (mole cm)

setOutputIncrement

public void setOutputIncrement(double _dt)

Sets the output increment for simulation data. The simulation must be stopped before calling this method.

Parameters:

_dt - output time increment in seconds

See Also:

setTimeIncrement(double)

setOwner

public void setOwner(edu.davidson.tools.SApplet owner)

Sets the owner for the SDataSource. (In this implementation, this method does not do anything.

Specified by:

setOwner in interface edu.davidson.tools.SDataSource

Parameters:

owner - owner of the data source

setPrecision

public void setPrecision(double _tol)

Sets the relative precision for the numerical calculations for the user-defined reaction order. Default is 0.0001

setRandom

public void setRandom(long rnd)

Sets the seed value for the random number generator. Allows users to obtain a reproducible set of values from the simulation. Valid only if a simulation is not in progress.

Parameters:

rnd - the seed value for the random number generator

setRateConstant

public void setRateConstant(double _rateConstant)

Sets the rate constant based upon species 0. The units should involve, where appropriate, mole, liter, and seconds. The simulation must not be running when this method is called.

setRateLaw

public void setRateLaw(double[] _exp)

Sets the rate law for the user-defined kinetics option (see setReactionOrder). The rate law is assumed to be of the form
rate = k [A]^a [B]^b ...
The parameter _exp is an array containing the rate law exponents for each species including products. If a species does not appear in the rate law, the exponent should be set to zero.

See Also:

setReactionOrder(int)

setRateLaw

public void setRateLaw(int _n,
                       double _exp)

Sets the exponent in the rate law for a given species for the user-defined kinetics option (see setReactionOrder). The rate law is assumed to be of the form
rate = k [A]^a [B]^b ...

Parameters:

_n - species number

_exp - exponent for species in the rate law

See Also:

setReactionOrder(int)

setReactionOrder

public void setReactionOrder(int _rxnOrder)

Sets the reaction order for the kinetics. The reaction involves at least two reactants, species 0 and species 1, which are contained in the two syringes. The rate law is formulated in terms of species 0. The user is responsible to making sure species 0 is the limiting reactant in cases where this issue is relevant.

The argument _rxnOrder has the following significance:
0 = zero-order kinetics
1 = first-order kinetics (default)
2 = second-order kinetics (species 0 only)
3 = second-order kinetics (species 0 and species 1)
4 = user-defined kinetics (use setRateLaw to define coefficients)

See Also:

setRateConstant(double), setConcentrationsA(double[]), setConcentrationsB(double[]), setConcentrations(double[], double[]), setFractions(double, double), setFractionsDelivered(double, double), setRateLaw(double[])

setStandardDeviation

public void setStandardDeviation(double _std)

Sets the standard deviation for the Gaussian error applied to the absorbance. The error is treated as an absolute error in the power or intensity of light reaching the detector. The relative error in the absorbance thus gets increasingly large as the absorbance approaches zero or as the absorbance becomes large.

If the standard deviation is set to 0.001, for example,

At A = 0.0100 the uncertainty is 0.0004

At A = 0.100 the uncertainty is 0.0005

At A = 1.00 the uncertainty is 0.004

At A = 2.00 the uncertainty is 0.04

At A = 3.00 the uncertainty is 0.4

Valid only if a simulation is not running.

Parameters:

_std - the standard deviation of the Gaussian noise

setTimeIncrement

public void setTimeIncrement(double _dt)

Sets the time increment for the simulation. The simulation must be stopped before calling this method. The start time must be an integer multiple of the time increment.

Parameters:

_dt - time increment in seconds

See Also:

setOutputIncrement(double), setStartTime(double)

setStartTime

public void setStartTime(double _time)

Sets the starting time for the chemical reaction. The starting time is the time required to depresses the syringe barrels to the specified position.

Parameters:

_time - starting time in seconds

setStopTime

public void setStopTime(double _time)

Sets the stopping time for the simulation reaction.

Parameters:

_time - stopping time in seconds

step

public void step(double dt,
                 double tm)

Calculates state of system at each step in the simulation. Called only by the clock.

Specified by:

step in interface edu.davidson.tools.SStepable